• Restrooms
• Wireless internet connection
• Pre-workshop survey https://forms.gle/wjKkYmZR1xHeYUot9
• Please accept the invitation from RStudio Cloud and create an account if you have not
• Open group note-taking http://bit.ly/notesRChem
• Link to slides

Hosted by ACS-CINF

Sponsored by ACS Publications

• Test technical setup
• Learn R Basics
• Apply R to a QSAR mini-project
• Write a report with R Markdown

• Your name
• Why are you interested in this workshop
• Anything else you’d like to share with the group

• Post sticky notes to the back of your laptop to signal the instructors and helpers

Hot pinky note means stop	Blue note means go

• Computational reproducibility and R
• R, RStudio, and RStudio Cloud overview
• Project Management in RStudio
• Basic programming in R
  • plotting a calibrarion curve
• Getting help

• Source of Irreproducibility
  • Rarely deliberate falsification
  • Unconscious investigator bias
    • Incorrect data or modified results to fit their preconceptions
  • bona fide results that’s difficult to repeat

https://doi.org/10.1002/anie.201606591

All the components below are required to reproduce the research publication

• Organization
  • e.g. folder structure, naming convention, bundle computing environment etc.
• Automation
  • e.g. script-based data analysis and writing etc.
• Documentation
  • e.g. Readme file, comments in data and scripts, ELN etc.
• Dissemination
  • e.g. repositories

• No lots of pointing and clicking - can re-run the script to reproduce the analysis
• Integrating with other tools to generate (and re-generate) your manuscript
• Interdisciplinary and extensible
• Working on data of all shapes and sizes
• Producing high-quality graphics
• Large and welcoming community
  • Stack Overflow(https://stackoverflow.com/)
  • RStudio Community(https://community.rstudio.com/))
• Open-source and cross-platform

• All info needed to write code in a single window
• Shortcuts, autocompletion, and highlighting for the major file types

• It remembers working directory and custom settings
• Steps in RStudio:
  • ‘File’ menu –> click on ‘New Project’.
  • Choose ‘Existing Directory’, then browse to the folder where you downloaded workshop data files.
  • Click on ‘Create Project’. An ’ .Rproj’ file is added to the project folder.
    
• Steps in RStudio Cloud
  • Click on ‘Start’ in front of the project “Student In-Class Practice”
  • An R Project has been created for you there.

• ‘data/’: use this folder to store your raw data and intermediate datasets you may create
  • Always keep a copy of your raw data
  • do as much of your data cleanup and preprocessing with scripts
• ‘scripts/’: use this folder for your R scripts for different analyses or plotting
• ‘figures/’: use this folder to save figures you plot using scripts
• ‘data_output/’: use this folder to save data files you obtained using scripts
• ‘documents/’: use this folder for your outlines, drafts, and other texts
• Practice: in RStudio Cloud / Student In-Class Practices
  • Use ‘New Folder’ button in the right bottom Files section to create a solder called ‘documents’

• Working directory: the place from where R will be looking for and saving the files
• RStudio will now set your working directory as the folder where your xxx.Rproj file lives
• Practice: in RStudio Cloud / Student In-Class Practices
  • Open scripts/RBasicsPractice.R
  • At line 6, typing “getwd()” and run it to identify the current working directory

• Use R as a calculator
• Assign value to a variable in the Environment
• Remove variables from the Environment
• Get tabulized data into the Environment as data frames
  • Calibration curve example
• Subset data frames
• Save data output
• Plot figure and linear fit
• Save plotted figures

• I know the name of the function I want to use, but I’m not sure how to use it
  • e.g. ?plot, args(lm)
• I want to use a function that does X, there must be a function for it but I don’t know which one…
  • e.g. ??color (call help.search() function)
• I am stuck… I get an error message that I don’t understand
  • e.g. Google, search stockoverflow.com with the tag [r]
  • Include computing environment info when asking questions - session.info()

This is an R Markdown presentation. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.

When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document.

• Bullet 1
• Bullet 2
• Bullet 3

summary(cars)

##      speed           dist       
##  Min.   : 4.0   Min.   :  2.00  
##  1st Qu.:12.0   1st Qu.: 26.00  
##  Median :15.0   Median : 36.00  
##  Mean   :15.4   Mean   : 42.98  
##  3rd Qu.:19.0   3rd Qu.: 56.00  
##  Max.   :25.0   Max.   :120.00